Mannich-type C-nucleosidations in the 5,8-diaza-7,9-dicarba-purine family

Article abstract of DOI:10.1021/ol048649m

(Chemical Equation Presented) C-Nucleosidation with cyclic iminium salts occurring under mild reaction conditions and affording C-nucleosides that are isosteric with N-nucleosides of natural purines is shown to be a consistent property of the entire family of 2,6-(oxo or amino)-disubstituted 5,8-diaza-7,9-dicarba-purines.

Full text of DOI:10.1021/ol048649m

ORGANIC
LETTERS
2004
Vol. 6, No. 21
3691-3694
Mannich-Type C-Nucleosidations in the
5,8-Diaza-7,9-dicarba-purine Family1
Bo Han,† Bernhard Jaun,† Ramanarayanan Krishnamurthy,‡,§ and
Albert Eschenmoser*,†,‡,
Laboratory of Organic Chemistry, Swiss Federal Institute of Technology,
Ho¨nggerberg, HCI-H309, CH-8093 Zu¨rich, Switzerland, and The Skaggs Institute for
Chemical Biology at The Scripps Research Institute, 10550 North Torrey Pines Road,
La Jolla, California 92037
eschenmoser@org.chem.ethz.ch
Received July 14, 2004
ABSTRACT
C-Nucleosidation with cyclic iminium salts occurring under mild reaction conditions and affording C-nucleosides that are isosteric with
N-nucleosides of natural purines is shown to be a consistent property of the entire family of 2,6-(oxo or amino)-disubstituted 5,8-diaza-7,9-
dicarba-purines.
In the context of ongoing studies directed toward a chemical
etiology of nucleic acid structure, we recently reported on
the synthesis2 and some chemical properties3 of the nucleo-
base-analogue 2,6-diamino-5,8-diaza-7,9-dicarba-purine 1.
The base is the 2,6-diamino derivative of a family of purinoid
heterocycles 1-4 that are isomeric to the family of the
natural purine nucleobases of which adenine and guanine
are the canonical members (Scheme 1). The heterocycles of
both families can be (formally) derived via isomeric gen-
erational pathways from the same ensembles of (potentially
prebiotic) building blocks HCN, NH2CN, and glycine nitrile
(see Scheme 2 in ref 2). Constitutionally corresponding
members of the two families possess functionally equivalent
recognition elements and are expected to show similar
reactivity and selectivity in Watson-Crick pairing. However,
they differ in their function as nucleophilic reaction partners
in nucleosidation reactions: 5,8-diaza-7,9-dicarba-purine
derivatives may undergo Mannich-type nucleosidation reac-
tions at position C-9 (purine numbering) to afford C-nucleo-
sides that are isosteric to conventional (N-9)-nucleosides of
the natural purine nucleobases. In a previous communication,
we have reported such C-nucleosidations of the 2,6-diamino
derivative 1.3 Those studies have now been extended to all
other members of the 5,8-diaza-7,9-dicarba-purine family (in-
cluding the adenine analogue), whereby it is found that the
propensity to undergo Mannich-type C-nucleosidations is in-
deed a consistent property within the family and not restricted
to the (most reactive) 2,6-diamino derivative.
Scheme 1. Members of the 5,8-Diaza-7,9-dicarba-purine
Family Juxtaposed to Corresponding Members of the Purine
Family
† Swiss Federal Institute of Technology.
‡ The Scripps Research Institute.
§ Fax: ++1-858-784-9573. E-mail: rkrishna@scripps.edu.
Fax: ++41-1-632-1043.
(1) Chemistry of R-Aminonitriles. Part 42. For Part 41, see: Ferencic,
M.; Reddy, G.; Wu, X.; Guntha, S.; Nandy, J.; Krishnamurthy, R.;
Eschenmoser, A. Chem. BiodiV. 2004, 1, 939.
(2) Wang, Z.; Huynh, H. K.; Han, Bo; Krishnamurthy, R.; Eschenmoser,
A. Org. Lett. 2003, 5, 2067.
(3) Han, Bo; Wang, Z.; Jaun, B.; Krishnamurthy, R.; Eschenmoser, A.
Org. Lett. 2003, 5, 2071.
10.1021/ol048649m CCC: $27.50
© 2004 American Chemical Society
Published on Web 09/18/2004

treatment of the product of cyclization with Meerwein’s
DMF-dimethylacetal.11,12
Scheme 2. Preparation of Guanine Analogue 2
The trichloromethyl group of 6 can also be converted to
an amino group of 9 by treatment with methanolic NH3; this
provides a convenient alternative to the previously reported2
synthesis of purinoid 1.
The preparations of 3 (the isoguanine analogue) and 4 (the
xanthine analogue) start from the preformed imidazole moi-
ety of the bicyclic heterocycles.13,2 Treatment of 5-amino-
imidazole in dioxane (prepared in situ by catalytic hydro-
genation of 5-nitro-imidazole13,14) with N-cyano-isocyanate-
dimethylacetal15,16 gives the bicyclic 2-methoxy-6-amino
derivative 10, the methoxy group of which is cleaved, pre-
sumably via N-protonation(s) followed by SN2 substitution
at the methyl carbon, to the carbonyl group of 3 by HBr in
acetic acid. Alternatively, reaction of 5-amino-imidazole in
dioxane with phenyloxycarbonyl-isocyanate17 affords the
intermediate 11, which smoothly cyclizes to 4 by heating in
ethanolic solution.
The methods used for preparing purinoids 2 (Scheme 2),
3 (Scheme 3), and 4 (Scheme 3) were chosen without re-
The isoguanine analogue 3 was obtained as a white solid
which, in contrast to 2, is only sparingly soluble in DMSO
and insoluble in H2O or CH3OH. The compound is thermally
stable to heating (in a closed tube) to 190 °C for 10 h. The
xanthine analogue 4 crystallized in colorless cubes from eth-
anol; it is soluble in DMSO, H2O, and CH3OH, and its con-
stitution was confirmed by X-ray analysis.10 The UV spectra
of 1-4, in which all absorption maxima are hypsochromic
relative to those of the corresponding purines, are reproduced
in Figure 1.9
Scheme 3. Preparation of 3 and 4
Scheme 4 summarizes our experiments on the C-nucleo-
sidation of the guanine analogue 2 with the previously
described pyrroline derivative 12.3 Treatment of 1.0 mol
equiv of 2 in DMF (c ) 0.2 M) with 1.1 mol equiv of 12 in
the presence of 1.1 proton equivalents (p-TsOH‚H2O) at
room temperature for 2 h afforded the corresponding
C-nucleosides essentially quantitatively, as revealed by direct
(NH)-protection of the reaction product in the reaction
mixture with (BOC)2O/Et3N followed by chromatography
course to the potentially etiological aspects that we associate
with these nucleobase analogues. N-Formyl-glycyl-guanidine
5, easily obtained from N-formyl-glycine ethylester4 and
guanidine,5 reacts with trichloroacetonitrile to give the
trichloromethyl-triazine derivative 6, which, following the
methodology described by Kelarev et al.,6 is hydrolytically
converted to 7. Remarkably, as well as satisfyingly, when
this N-formyl-aminomethyl-triazine is treated with concen-
trated H2SO4 at 100 °C, a procedure reported in the literature
for the cyclization of other keto-amino-triazine derivatives,7
dehydrative cyclization proceeds regioselectively and gives
the guanine analogue 2 in high yield; the isomeric cyclization
product is not observed.8 1H and 13C NMR spectra of 2 are
compatible with the assigned constitution;9 the proof, hard
to come by spectroscopically, is based on X-ray structure
analysis10 of the derivative 8, formed in high yield by mild
(8) Considering the harsh reaction conditions (concentrated H2SO4, 100°
C) and the multitude of protonation sites in the substrate, we refrain from
attempting to rationalize the observed regioselectivity of the cyclization.
(9) NMR and mass spectral properties, see Supporting Information.
(10) X-ray structure analysis of 4 and 8 was carried out by Dr. Bernd
Schweizer, ETH-Z. Crystallographic data for the structure has been deposited
with the Cambridge Crystallographic Data Center as deposition no. CCDC
242452 for 8 and no. CCDC 242453 for 4. Copies of the data can be
obtained, free of charge, on application to the CCDC, 12 Union Rd.,
Cambridge CB12 1EZ, UK (fax: +44 (1233) 336 0333; e-mail: deposit@
ccdc.cam.ac.uk). Data of 4 and 8 can be found in Supporting Information.
(11) Reaction of 2 with DMF-dimethylacetal in methanol at room
temperature produces, besides 8, small amounts of a side product containing
an additional dimethylamino-methylidene group at carbon C-9.
(12) Koch, G. (Novartis AG, Basel) Private communication: Underiva-
tized 2 could be obtained in crystalline form and as such subjected to X-ray
structure analysis (work by G. Koch and B. Wagner (Novartis)).
(13) Al-Shaar, A. H. M.; Chambers, R. K.; Gilmour, D. W.; Lythgoe,
D. J.; McClenaghan, I.; Ramsden, C. A. J. Chem. Soc., Perkin Trans. 1
1992, 2789.
(4) Martin, P. K.; Matthews, H. R.; Rapoport, H.; Thyagarajan, G. J.
Org. Chem. 1968, 33, 3758.
(5) Procedure for the preparation of N-formyl-L-valyl-guanidine by:
Hoffmann, E.; Diller, D. Can. J. Chem. 1965, 43, 3103.
(6) Kelarev, V. I.; Ammar Dibi; Lunin, A. F. Chem. Heterocycl. Compd.
(NY) 1985, 21, 1284; English translation from Khim. Geterotsikl. Soedin.
1985, 21, 1557.
(14) Rabinowitz, J. C. J. Biol. Chem. 1956, 218, 175.
(15) Prepared by heating cyanamide in tetramethyl orthocarbonate at 95
°C in 76% yield (mp 56-58° C) according to Kantlehner et al.16 but using
tetramethyl- instead of tetraethyl-orthocarbonate in order to avoid the for-
mation of a mixture of O- and N-ethylated isomers (see procedure in Sup-
porting Information).
(16) Kantlehner, W.; Maier, T.; Lo¨ffler, W.; Kapassakalidis, J. J. Liebigs
Ann. Chem. 1982, 507.
(7) Kim, S.-H.; Bartholomew, D. G.; Allen, L. B.; Robins, R. K.;
Revankar, G. R.; Dea, P. J. Med. Chem. 1978, 21, 883.
(17) Rao, P.; Benner, S. A. J. Org. Chem. 2001, 66, 5012.
3692
Org. Lett., Vol. 6, No. 21, 2004

Scheme 4. C-Nucleosidation of Guanine Analogue 2 with
BOC-Protected (3R)-trans-3,4-Diamino-1-pyrroline 12
a Yields for 14 calculated as tetra-HCl-salts.
Figure 1. UV absorption spectra of purinoids 1-4 (c ) 2.33-
2.52 × 10-4 M in 0.1 M, pH 7, aq phosphate buffer, rt). 1: ꢀ (220
nm) ) 23 300; λmax ) 265 nm (ꢀ ) 7900); ꢀ (ca 310 nm) ) 1900.
2: ꢀ (220 nm) ) 10 200; λmax ) 261 nm (ꢀ ) 7300). 3: ꢀ (220
nm) ) 24 400; λsh ) 240 nm (ꢀ ) 5200); ꢀ (ca 290 nm) ) 1000.
4: ꢀ (220 nm) ) 4300; λmax ) 237 nm (ꢀ ) 5900).
a qualitative comparison of the relative reactivity of all
purinoids investigated, including the previously described3
diamino derivative 1, as well as its 2-deamino- () adenine)
analogue.13 In four of the five cases, (protected) epimeric
C-nucleosides have been separated by column chromatog-
raphy.9 The purinoids 1-4 and their adenine analogue
2-deamino-113 all undergo the C-nucleosidation with 15 in
comparable yields under reaction conditions that are identical
with the exception of reaction times. These vary within a
factor of roughly 100 in the order 1 > 2 ∼ 3 > 4 > (2-
deamino)-1, with the 2,6-diamino-purinoid 1 as the fastest
and its 2-deamino derivative as the slowest member of the
family. What may appear to be surprising in this sequence,
namely, that the two oxo-amino-members 2 and 3 and even
the dioxo-member 4 undergo electrophilic substitution at
position C-9 faster than the adenine analogue, is a reminder
of the more pronounced 10-π-electron aromaticity of mem-
bers that bear only amino groups as substituents as against
purinoids containing lactam groups. Mechanistic reasoning
predicts that there should be an inverse relationship between
the propensity of purinoids to undergo electrophilic C-
nucleosidation and the stability of corresponding C-nucleo-
sides. Experimental data seem to confirm this expectation:
the nucleosides 14R and 14â (Scheme 4) equilibrate at room
temperature within weeks at pH 1.7 and within months at
pH 11.7; the corresponding nucleosides derived from 13 do
so within hours (rt) at pH 1.9 and within weeks at pH 11.3.
Of the four purinoids 1-4, the isoguanine analogue 3
deserves a special comment with regard to its constitution.
Isoguanine of the natural purine family exists, in contrast to
guanine, as a mixture of tautomers in which the NH(3)-lac-
tam tautomer (Figure 2) is not reported to be among those
observed.20 The coexistence (or accessibility) of this specific
tautomer, however, has been documented in base-pairing
studies in the homo-DNA21 as well the pyranosyl-RNA
series22 by the observation of robust duplexes, the formation
of which must be interpreted to rely on guanine-isoguanine
base-pairs of type A (Figure 2). The type of isoguanine tau-
tomer required in such purine-purine base-pairs becomes
the only possible lactam-type tautomer in the case of the
isoguanine analogue 3. We therefore can foresee the exist-
ence of informational oligomers that may contain only puri-
of the epimeric nucleosides to give pure R-epimer 13R in
70% and pure epimer 13â in 22% yield. The assignment of
1
constitution rests on mass and H/13C NMR spectroscopic
data and the assignment of configuration on NMR data
observed for the corresponding deprotected nucleosides 14R
and 14â (see below).
Keeping samples of 13R or 13â in methanolic HCl
(saturated at room temperature) for 30 min and subsequently
removing volatiles by evaporation under reduced pressure
afforded the anomeric nucleosides 14R and 14â, respectively,
as hydrochlorides18 in the form of water-soluble white solids.
The assignment of their configuration at the anomeric centers
is based on NMR (J values and NOE) data.19
The two anomers 14R and 14â are configurationally stable
under the conditions of deprotection (NMR). They slowly
epimerize in D2O solution (1H NMR, pH 1.7) at room
temperature reaching an equilibrium composition of 14R:
14â ∼3:1 within about 2 weeks. In alkaline D2O solution
(NaOH, pH ) 11.8), at room temperature they reach
equilibrium after about 2 months. The protected nucleosides
13R and 13â are configurationally stable in DMSO at room
temperature; yet when heated in DMSO-d6 to 100 °C, they
equilibrate to a composition of 13R:13â ∼1.4:1 within 1 day
(1H NMR).
C-Nucleosidations of the purinoids 3 and 4 with (trimeric)
pyrroline 153 are summarized in Scheme 5, which also gives
(18) Estimated (by weight, after drying at room temperature/HV/
overnight) to be tris- or tetrahydrochlorides; pH of solutions in H2O ∼ 1.7
(0.072 M).
(19) Minor isomer 14â exhibits coupling constants J1′2′ ) 7.9 Hz, J2′3′
) 6.7 Hz, J3′4′si ) 9.3 Hz, J3′4′re ) 6.0 Hz. NOEs H1′-H2′ (m), H1′-H4′re
(w), H3′-H4′si (s) indicate that H1′ is cis to both H2′ and H4′re. For the
major isomer 14R, coupling constants J1′2′ ) 7.4 Hz, J2′3′ ) 5.8 Hz, J3′4′si
) 8.8 Hz, J3′4′re ) 6.0 Hz together with NOEs H1′-H2′ (w), H1′-H3′
(w), H1′-H4′si (w), H2′-H4′re (m), and H3′-H4′si (s) are consistent with
H1′ being trans to H2′ and cis to H4′si. The similar coupling constants
indicate that both epimers have the same predominant conformation of the
five-membered ring with a dihedral angle H1′-C1′-C2′-H2′ near 150°
for the R-isomer and near 10° for the â-isomer.
Org. Lett., Vol. 6, No. 21, 2004
3693

Scheme 5. C-Nucleosidation of 1-4 and 2-Deamino-1 (Adenine Analogue) with (3R)-trans-3,4-Dibenzoyl-1-pyrroline 15
a Reaction times of step a. bYields over steps a and b. cEpimeric ratios determined by integration of H-1′ and H-4′re signals in the NMR.9
dSeparation yields.
noids 1-4 as nucleobases and where duplexation and the
function of sequence recognition is exclusively based on
purinoid-purinoid base-pairs of types B and C (Figure 2).
them is their chemical versatility for the task of attaching
sets of complementary recognition elements to functional
groups in any kind of substrate.
Acknowledgment. The work was supported by Novartis
AG (Basel) and the Skaggs Research Foundation. We thank
Dr. Guido Koch and Dr. J. Zimmermann (Novartis) for their
interest in, and support of, this work.
Supporting Information Available: Procedures and data
for purinoids 2-4, as well as their nucleosidation reactions
with 12 and 15; CIF files for X-ray structures of compounds
4 and 8. This material is available free of charge via the
Internet at http://pubs.acs.org.
OL048649M
(20) Sepiol, J.; Kazimierczuk, Z.; Shugar, D. Z. Naturforsch. Part C 1976,
31, 361. Seela, F.; Wei, C.; Kazimierczuk, Z. HelV. Chim. Acta 1995, 78,
1843. See also discussion on the tautomerism in isoguanine in ref 21 (p
438 ff).
(21) Groebke, K.; Hunziker, J.; Fraser, W.; Peng, L.; Diederichsen, U.;
Zimmermann, K.; Holzner, A.; Leumann, C.; Eschenmoser, A. HelV. Chim.
Acta 1998, 81, 375.
(22) Krishnamurthy, R.; Pitsch, S.; Minton, M.; Miculka, C.; Windhab,
N.; Eschenmoser, A. Angew. Chem., Int. Ed. Engl. 1996, 35, 1537.
(23) Oro´, J. Biochem. Biophys. Res. Commun. 1960, 2, 407. Ferris, J.
P.; Hagan, W. J., Jr. Tetrahedron 1984, 40, 1093 (review). Miyakawa, S.;
Cleaves, H. J.; Miller, S. L. Orig. Life EVol. Biosphere 2002, 32, 209. Orgel,
L. E. Orig. Life. EVol. Biosphere 2004, 34, 361.
(24) Leonard, N. J.; Laursen, R. A. Biochemistry 1965, 4, 354. Seela,
F.; Driller, H. Nucleic Acids Res. 1985, 13, 911. Switzer, C.; Moroney, S.
E.; Benner, S. A. J. Am. Chem. Soc. 1989, 111, 8322. Schweitzer, B. A.,
Kool, E. T. J. Am. Chem. Soc. 1995, 117, 1863. McMinn, D. L.; Ogawa,
A. K.; Wu, Y.; Liu, J.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc.
1999, 121, 11585.
(25) Liu, H.; Gao, J.; Lynch, S. R.; Saito, Y. D.; Maynard, L.; Kool, E.
T. Science 2003, 302, 868. Seela, F.; Debelak, H. J. Org. Chem. 2001, 66,
3303. Geyer, C. R.; Battersby, T. R.; Benner, S. A. Structure 2003, 11,
1485 (review).
(26) Leonard, N. J. CRC Crit. ReV. Biochem. 1984, 15, 125. Evans, G.
B.; Furneaux, R. H.; Gainsford, G. J.; Hanson, J. C.; Kicska, G. A.; Sauve,
A. A.; Schramm, V. L.; Tyler, P. C. J. Med. Chem. 2003, 46, 155. Chang,
Y.-T.; Gray, N. S.; Rosania, G. R.; Sutherlin, D. P.; Kwon, S.; Norman, T.
C.; Sarohia, R.; Leost, M.; Meijer, L.; Schultz, P. G. Chem. Biol. 1999, 6, 361.
(27) Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. Nature
1990, 343, 33. Kool, E. T. Acc. Chem. Res. 2002, 35, 936.
Figure 2. Purinoids 1-4 are expected to be able to act as
nucleobases forming two Watson-Crick-type base-pairs B and C.
Whether the chemistry of the purinoid family 1-4 is
potentially relevant in the etiological context that provided
the stimulus for the present investigation in the first place
will primarily depend on whether members of the family
can be generated and, if so, under what conditions, from
potentially prebiotic precursor molecules of the canonical
nucleobases.23 The question is to be answered experimentally.
Irrespective of the outcome of such experiments, the pu-
rinoids deserve attention from a purely chemical point of
view. They are special members of a growing list of artificial
purinoid nucleobase variants24 that are of interest as vehicles
of research in informational chemistry,25 medicinal chem-
istry,7,26 and chemical biology.27 What is deemed special in
3694
Org. Lett., Vol. 6, No. 21, 2004